Isolation and characterization of cyanobacteria from extreme environment is important in identifying novel molecules and understanding the mechanisms underlying the tolerance. Therefore in the present study an attempt was made to isolate, identify and characterize cyanobacteria from Runn of Kutch experiencing high levels of salinity. On the basis of microscopic, morphological and cultural characteristics the identified cyanobacterial strains included Anabaena, Nostoc, Westielliopsis, Phormidiumand Synechocystis. Further analysis on the basis of 16S r DNA sequence and BLAST analysis confirmed their identity. Among the ten identified strains, seven strains such as belonging to Anabaena, Phormidium, Nostoc and Westielliopsis showed the presence of mycosporine like amino acids. Growth, cellular constituents and parameters of nitrogen assimilation in these strains were studied and showed significant differences. The present investigation helped in the identification of cyanobacterial strains producing mycosporine like amino acids which are novel compounds involved in stress tolerance.